From Local to Cluster: A Unified Framework for Causal Discovery with Latent Variables

Discovering the direct causes and effects of a target variable from observational data is a fundamental problem in causal discovery, with broad applications in domains such as gene regulatory analysis and biomedical research. Existing causal discovery methods either learn a global causal structure, which incurs substantial computational cost, or assume the absence of latent variables and selection bias, assumptions that are often violated in real-world settings. Motivated by these challenges, we study local causal structure learning in the presence of latent variables and selection bias. Specifically, we first characterize a local region that enables target-specific causal discovery without recovering the entire global structure. We then establish a theoretical bridge between causal information learned from the observed distribution induced on this local region and the corresponding information in the global causal structure. Building on these foundations, we propose LoCaLS, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias. Extensive experiments on random and real-world structures demonstrate that the proposed method consistently achieves higher structural accuracy than existing local methods while requiring substantially less computational effort than state-of-the-art global methods. Furthermore, applications to two real-world gene expression datasets reveal biologically plausible target-specific causal structures, demonstrating its practical applicability in large-scale biological data analysis.

Constraint-based causal discovery is widely used for learning causal structures, but heavy reliance on conditional independence (CI) testing makes it computationally expensive in high-dimensional settings. To mitigate this limitation, many divide-and-conquer frameworks have been proposed, but most assume causal sufficiency, i.e., no latent variables. In this paper, we show that divide-and-conquer strategies can be theoretically generalized beyond causal sufficiency to settings with latent variables. Specifically, we propose a recursive decomposition framework, termed DiCoLa, that enables divide-and-conquer causal discovery in the presence of latent variables. It recursively decomposes the global learning task into smaller subproblems and integrates their solutions through a principled reconstruction step to recover the global structure. We theoretically establish the soundness and completeness of the proposed framework. Extensive experiments on synthetic data demonstrate that our approach significantly improves computational efficiency across a range of causal discovery algorithms, while experiments on a real-world dataset further illustrate its practical effectiveness.

Causal discovery aims to learn causal structures up to certain symmetries. Diverse populations or changing environments give rise to heterogeneous data in the following sense: each population/environment is a ``source'' which idiosyncratically determines the forms of causal effects. From this perspective, the source is a latent common cause for every observed variable. While some methods for causal discovery can work around latent confounding in special cases, a global confounder poses a significant challenge. The only known ways to deal with latent global confounding involve making assumptions that limit structural equations and/or noise functions. We demonstrate that globally confounded causal structures can still be identified with arbitrary structural equations and noise functions, so long as the number of latent classes remains small relative to the size and sparsity of the underlying DAG. The approach relies on agglomerating variables into large-enough matrices of moments, whose ranks directly reveal graphical properties of the causal structure. We also provide a statistical test to test the rank of these matrices.